8FL0 image
Deposition Date 2022-12-21
Release Date 2023-07-12
Last Version Date 2024-06-19
Entry Detail
PDB ID:
8FL0
Keywords:
Title:
Human nucleolar pre-60S ribosomal subunit (State H)
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
2.91 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L12
Gene (Uniprot):RPL12
Chain IDs:A (auth: BA)
Chain Length:165
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:28S rRNA
Chain IDs:B (auth: L3)
Chain Length:5070
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:C (auth: L4)
Chain Length:121
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L11
Gene (Uniprot):RPL11
Chain IDs:D (auth: L5)
Chain Length:178
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13a
Gene (Uniprot):RPL13A
Chain IDs:E (auth: L7)
Chain Length:203
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L14
Gene (Uniprot):RPL14
Chain IDs:F (auth: L8)
Chain Length:215
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18
Gene (Uniprot):RPL18
Chain IDs:G (auth: LB)
Chain Length:188
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18a
Gene (Uniprot):RPL18A
Chain IDs:H (auth: LC)
Chain Length:176
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21
Gene (Uniprot):RPL21
Chain IDs:I (auth: LE)
Chain Length:160
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23
Gene (Uniprot):RPL23
Chain IDs:J (auth: LG)
Chain Length:140
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Gene (Uniprot):RPL28
Chain IDs:K (auth: LL)
Chain Length:137
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Gene (Uniprot):RPL3
Chain IDs:L (auth: LN)
Chain Length:403
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L32
Gene (Uniprot):RPL32
Chain IDs:M (auth: LQ)
Chain Length:135
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35a
Gene (Uniprot):RPL35A
Chain IDs:N (auth: LT)
Chain Length:110
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Guanine nucleotide-binding protein-like 3
Gene (Uniprot):GNL3
Chain IDs:O (auth: NB)
Chain Length:549
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Nucleolar GTP-binding protein 2
Gene (Uniprot):GNL2
Chain IDs:P (auth: NC)
Chain Length:731
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome production factor 2 homolog
Gene (Uniprot):RPF2
Chain IDs:Q (auth: ND)
Chain Length:306
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis protein NSA2 homolog
Gene (Uniprot):NSA2
Chain IDs:R (auth: NF)
Chain Length:260
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Notchless protein homolog 1
Gene (Uniprot):NLE1
Chain IDs:S (auth: NJ)
Chain Length:485
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Protein LLP homolog
Gene (Uniprot):LLPH
Chain IDs:T (auth: NK)
Chain Length:129
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Coiled-coil domain-containing protein 86
Gene (Uniprot):CCDC86
Chain IDs:U (auth: NZ)
Chain Length:360
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4
Gene (Uniprot):RPL4
Chain IDs:V (auth: SA)
Chain Length:427
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Gene (Uniprot):RPL5
Chain IDs:W (auth: SB)
Chain Length:297
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L6
Gene (Uniprot):RPL6
Chain IDs:X (auth: SC)
Chain Length:288
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7
Gene (Uniprot):RPL7
Chain IDs:Y (auth: SD)
Chain Length:248
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9
Gene (Uniprot):RPL9, RPL9P7, RPL9P8, RPL9P9
Chain IDs:Z (auth: SG)
Chain Length:192
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Eukaryotic translation initiation factor 6
Gene (Uniprot):EIF6
Chain IDs:AA (auth: SK)
Chain Length:245
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:mRNA turnover protein 4 homolog
Gene (Uniprot):MRTO4
Chain IDs:BA (auth: SQ)
Chain Length:239
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:GTP-binding protein 4
Gene (Uniprot):GTPBP4
Chain IDs:CA (auth: SR)
Chain Length:634
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Ribosome biogenesis regulatory protein homolog
Gene (Uniprot):RRS1
Chain IDs:DA (auth: ST)
Chain Length:365
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Probable ribosome biogenesis protein RLP24
Gene (Uniprot):RSL24D1
Chain IDs:EA (auth: SV)
Chain Length:163
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Principles of human pre-60 S biogenesis.
Science 381 eadh3892 eadh3892 (2023)
PMID: 37410842 DOI: 10.1126/science.adh3892

Abstact

During the early stages of human large ribosomal subunit (60S) biogenesis, an ensemble of assembly factors establishes and fine-tunes the essential RNA functional centers of pre-60S particles by an unknown mechanism. Here, we report a series of cryo-electron microscopy structures of human nucleolar and nuclear pre-60S assembly intermediates at resolutions of 2.5 to 3.2 angstroms. These structures show how protein interaction hubs tether assembly factor complexes to nucleolar particles and how guanosine triphosphatases and adenosine triphosphatase couple irreversible nucleotide hydrolysis steps to the installation of functional centers. Nuclear stages highlight how a conserved RNA-processing complex, the rixosome, couples large-scale RNA conformational changes with pre-ribosomal RNA processing by the RNA degradation machinery. Our ensemble of human pre-60S particles provides a rich foundation with which to elucidate the molecular principles of ribosome formation.

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